BiomFormat

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The BIOM file format (canonically pronounced “biome”) is designed to be a general-use format for representing biological sample by observation contingency tables. https://www.bioconductor.org/packages/release/bioc/vignettes/biomformat/inst/doc/biomformat.html.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

library("biomformat"); packageVersion("biomformat")

## [1] '1.20.0'

## ----read-biom-examples-------------------------------------------------------
min_dense_file   = system.file("extdata", "min_dense_otu_table.biom", 
                               package = "biomformat")
min_sparse_file  = system.file("extdata", "min_sparse_otu_table.biom", 
                               package = "biomformat")
rich_dense_file  = system.file("extdata", "rich_dense_otu_table.biom", 
                               package = "biomformat")
rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom", 
                               package = "biomformat")
min_dense_file   = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat")
rich_dense_char  = system.file("extdata", "rich_dense_char.biom", package = "biomformat")
rich_sparse_char  = system.file("extdata", "rich_sparse_char.biom", package = "biomformat")
x1 = read_biom(min_dense_file)
x2 = read_biom(min_sparse_file)
x3 = read_biom(rich_dense_file)
x4 = read_biom(rich_sparse_file)
x5 = read_biom(rich_dense_char)
x6 = read_biom(rich_sparse_char)

## ----accessor-examples-table--------------------------------------------------
biom_data(x1)

## 5 x 6 Matrix of class "dgeMatrix"
##          Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
## GG_OTU_1       0       0       1       0       0       0
## GG_OTU_2       5       1       0       2       3       1
## GG_OTU_3       0       0       1       4       2       0
## GG_OTU_4       2       1       1       0       0       1
## GG_OTU_5       0       1       1       0       0       0

biom_data(x2)

## 5 x 6 sparse Matrix of class "dgCMatrix"
##          Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
## GG_OTU_1       .       .       1       .       .       .
## GG_OTU_2       5       1       .       2       3       1
## GG_OTU_3       .       .       1       4       .       2
## GG_OTU_4       2       1       1       .       .       1
## GG_OTU_5       .       1       1       .       .       .

## ----matrix-coercion----------------------------------------------------------
as(biom_data(x2), "matrix")

##          Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
## GG_OTU_1       0       0       1       0       0       0
## GG_OTU_2       5       1       0       2       3       1
## GG_OTU_3       0       0       1       4       0       2
## GG_OTU_4       2       1       1       0       0       1
## GG_OTU_5       0       1       1       0       0       0

## ----observ-meta--------------------------------------------------------------
observation_metadata(x1)

## NULL

observation_metadata(x2)

## NULL

observation_metadata(x3)

observation_metadata(x4)[1:2, 1:3]

class(observation_metadata(x4))

## [1] "data.frame"

Including Plots

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## NULL

## NULL

## [1] "data.frame"

## [1] FALSE

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